GATK 2.8 Realigner Target Creator reference genome issue
Hello everyone, I want to use Realigner Target Creator provided in the toolshed with the GATK version2.8. Unfortunately, I have a strange error : "Failed runtime validation of Using reference genome (A...
View ArticleCriteria for filtering OxoG artifacts in Mutect2
Hello, What filter criteria should one apply to filter out OxoG artifacts for M2 calls? Elsewhere in the forum, it is mentioned that "You can use the FOXOG annotation as an estimate of whether the...
View ArticleWhat's in the resource bundle and how can I get it?
NOTE: we recently made some changes to the bundle on the FTP server; see the Resource Bundle page for details. In a nutshell: minor directory structure changes, and Hg38 bundle now mirrors the cloud...
View ArticleUsing CombineVariants to update GT fields with phasing information
Hi GATK Team I was wondering whether you guys have developed capability for updating GT fields with phasing information contained in another VCF? For instance, I generated phased genotypes using...
View ArticleHomozygous reference genotype is called in native mode but uncalled in...
Hi, I'm having an issue with HaplotypeCaller in -ERC GVCF mode. Our pipeline uses GATK Best Practices (version 3.5) with GVCF mode and normally we don't have many issues, but with this particular...
View Articlebad input error on the PrintRead step
To detect the mutation on the bam file, I used GATK to calibrate the file currently. However, only one showed this kind of error when I used PrintRead mode. The version of program is 3.5 Input: java...
View Article--input-prior default value?
Happy new year GATK team! Quick question... What are the defaults for --input-prior of UG, HC and GG mentioned here:...
View ArticleGATk 3.6 / VariantRecalibrator is getting slower and slower.
Hi GATK team, I'm running VariantRecalibrator (v 3.6) on SNPs on ~300 Sample WGS. java -Xmx5g -Djava.io.tmpdir=... -jar GenomeAnalysisTK.jar -T VariantRecalibrator -R all_chr.fasta -input...
View ArticleTranches plot issue
Hi Geraldine, I think that this question has been asked before but I cannot find the way to fix the problem. I have just run VariantRecalibrator tool, and I'm getting this (see attached file) tranches...
View ArticleCRAM support in GATK 3.7 is broken
I have not been able to get GATK 3.7 HaplotypeCaller to work with CRAM files at all (it has a 100% failure rate so far with our whole genome CRAMs). Based on my analysis of the problem, I don't think...
View ArticleGATK (v 3.5) VariantAnnotator ERROR: potential bug?
Hi, I am using VariantAnnotator and, among other annotations, I would like to add also the allelic frequency of my SNPs in 1000G to the resulting annotated .vcf file. I did this through the following...
View ArticleFiltering out M2 Mutect Calls made in regions where only 1 type of read...
Hello, I have applied filter criteria based on OxoG as discussed in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3616734/. However, I have regions that are present consistently across samples (and...
View ArticleOncotator Most Recent Version and Data Source
Where can I download the most recent version of Oncotator, and data source? v1.9.1.0?
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How long does it take, Part 2
A while back, I posted this article about work done by the Intel Bio Team to benchmark the speed and resource utilization of each step in the per-sample segment of the germline variation pipeline...
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How long does it take to run the GATK Best Practices?
When you're setting up a variant discovery pipeline, you face two problems: deciding what tools to run (with what options), and how to run them efficiently so that it doesn't take forever. Between our...
View ArticleHaplotyper memory issue
Hi. I am running Haplotyper with the below command. java -jar /usr/local/lib/GenomeAnalysisTK.jar -T HaplotypeCaller -R /media/data1/02_SNP_flanking_GC_content/am45new.fasta -nct 1 -I...
View ArticleRefseq annotation for Oncotator
Hi, Oncotator uses GENCODE/ENSEMBL transcripts and annotations for hg19. Is there a way I could use RefSeq Transcript annotations instead. I am talking about 'cChange' and 'pChange' annotations. I do...
View Articleselecting/intersecting variants
Hello GATK, I have a WGS experiment of 3 genotypes from my favorite non-model organism for which I called variants based on GATK best practices (a pain for non-models!). I am interested in finding...
View Articlecan't see best practice
hi guys. why i can't see the best practice pages in the following link: https://software.broadinstitute.org/gatk/best-practices/mutect1.php I can see it in the gerline , but not the somatic. thanks omri
View ArticleMeaning of MQ value
Dear GATK team, I am wondering: is there an easy way to interpret the MQ value? I know that MQ stands for the 'root mean square (RMS) of Mapping Quality', and that it gives 'an estimation of the...
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